Journal of thoracic disease最新文献

{"title":"Correlation analysis of hematocrit level and coronary heart disease in patients with chest pain: a case-control study.","authors":"Jiahong Xie, Hongshuai Cao, Dongxu Jin, Yuxin Wang, Xiaolu Li, Matthew Budoff, Hongfeng Jiang, Jingyi Ren","doi":"10.21037/jtd-2025-645","DOIUrl":"10.21037/jtd-2025-645","url":null,"abstract":"<p><strong>Background: </strong>At present, there is controversy about whether hematocrit (HCT) is a risk factor for coronary heart disease (CHD). We try to explore the effect of low or high HCT on CHD, and analyze its mechanism from the perspective of hemodynamics.</p><p><strong>Methods: </strong>According to the exclusion criteria, a total of 3,200 patients who underwent coronary angiography or coronary computed tomography angiography (CTA) for typical post-exercise chest pain/dyspnea; atypical chest pain; or noncardiac chest pain or asymptomatic at Beijing Anzhen Hospital Affiliated to Capital Medical University from October 2019 to October 2021 were selected as research subjects. A coronary artery stenosis of 50% was used as the criterion for determining CHD. A total of 1,660 patients with coronary artery stenosis greater than 50% were selected as the CHD group and 1,540 adults with coronary artery stenosis less than 50% were selected as the non-CHD group. The clinical data, including HCT, were subjected to non-parametric tests and chi-square tests. The relationship between HCT and CHD was statistically analyzed using logistic regression. Wall shear stress (WSS) is obtained through fluent software combined with Navier-Stokes (NS) equation calculation.</p><p><strong>Results: </strong>Multivariate logistic regression analysis showed that HCT was an independent risk factor for CHD [risk ratio (RR) 1.108, 95% confidence interval (CI): 1.084-1.133, P<0.001]. The area under the receiver operating characteristic (ROC) curve for the ability of HCT to predict CHD events was 0.726. The cut-off value was 44.13, with specificity of 0.701 and sensitivity of 0.702. The results of a computational fluid dynamics simulation demonstrated that the magnitude of HCT is positively correlated with the WSS. When HCT exceeds 50%, the WSS of the stenosis site reaches 42 Pa, which may lead to endothelial denudation and further damage to the blood vessel, resulting in plaque rupture.</p><p><strong>Conclusions: </strong>HCT is one of the risk factors for CHD. Combining HCT with traditional risk factors may be helpful for non-invasive diagnosis of CHD. In addition, the level of HCT may also help to judge the future prognosis of patients with coronary artery stenosis greater than 50% without revascularization, providing a new potential target for future clinical treatment of CHD.</p>","PeriodicalId":17542,"journal":{"name":"Journal of thoracic disease","volume":"17 4","pages":"2492-2502"},"PeriodicalIF":2.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090147/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Defining lung adenocarcinoma subtypes with glucocorticoid-related genes and constructing a prognostic index for immunotherapy guidance.","authors":"Hongguang Tang, Jianhua Zhu, Yongliang Wang, Jianjie Zhang, Jianwei Zhou, Zhoumiao Chen","doi":"10.21037/jtd-24-1083","DOIUrl":"10.21037/jtd-24-1083","url":null,"abstract":"<p><strong>Background: </strong>Several studies have shown that glucocorticoid-related genes (GCGs) play a crucial role in cancer. However, the mechanism of GCGs in lung adenocarcinoma (LUAD) is not fully understood. This study aimed to identify distinct subtypes of LUAD by integrating GCGs and to develop prognostic models for precise prognosis prediction and immunotherapy guidance.</p><p><strong>Methods: </strong>In this study, sample data of LUAD were collected from The Cancer Genome Atlas (TCGA) database, and unsupervised clustering was used to identify LUAD subtypes with different GCGs characteristics. Survival-related genes were screened by differential expression analysis and protein-protein interaction (PPI) network analysis. After that, the least absolute shrinkage and selection operator (LASSO) combined with Cox regression analysis was used to establish the prognosis model. Differences in the immune microenvironment of different risk groups were analyzed, and Tumor Immune Dysfunction and Exclusion (TIDE) was used to predict the response of patients to immunotherapy. Finally, the CellMiner database was used to predict potential drugs.</p><p><strong>Results: </strong>Two subtypes of LUAD were identified, namely cluster 1 (high survival rate) and cluster 2 (low survival rate). A prognostic model was constructed based on 9 characteristic genes, including <i>CLCA1</i>, <i>CYP17A1</i>, <i>GRIA2</i>, <i>IGFBP1</i>, <i>IGF2BP1</i>, <i>NTSR1</i>, <i>RPE65</i>, <i>VGF</i>, and <i>WNT16</i>, and the prognosis of LUAD patients was positively predicted. There were differences in the immune microenvironment of different risk LUAD patients, and high-risk LUAD patients may benefit less from immunotherapy. BGB-283 was a candidate for LUAD targeting VGF.</p><p><strong>Conclusions: </strong>Our study elucidates the impact of GCGs on LUAD prognosis and immune responses, offering insights for prognostic forecasting and immunotherapeutic strategies for LUAD patients.</p>","PeriodicalId":17542,"journal":{"name":"Journal of thoracic disease","volume":"17 4","pages":"1888-1905"},"PeriodicalIF":2.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>SMARCA4</i>-deficient undifferentiated thoracic tumor: a case report and literature review.","authors":"Zhenzhen Liu, Na Li, Jiaqiu Liu, Jielin Li, Jingfei Sun, Franz Zehentmayr, Igor Gomez-Randulfe, Yuan Liang","doi":"10.21037/jtd-2025-541","DOIUrl":"10.21037/jtd-2025-541","url":null,"abstract":"<p><strong>Background: </strong><i>SMARCA4</i>-deficient undifferentiated thoracic tumor (<i>SMARCA4</i>-UT) are very aggressive high-grade malignant tumors associated with poor prognosis. It is typically diagnosed at an advanced stage. Response to conventional therapeutic approaches is particularly poor and there is no specific targeted drug for this mutation site. Currently, there are no guidelines regarding the standard treatment for this disease.</p><p><strong>Case description: </strong>In November 2021, a 71-year-old Chinese male was diagnosed with metastatic <i>SMARCA4</i>-UT in liver and brain. Molecular analysis showed a <i>TP53</i> mutation in exon 10 and a programmed death-ligand 1 (PD-L1) tumor proportion score (TPS) of <1%. From January 2022, the patient received a combination of camrelizumab, bevacizumab, pemetrexed, and carboplatin for four cycles, followed by camrelizumab, bevacizumab, and pemetrexed maintenance therapy for 31 cycles. The last treatment was on June 25, 2024. Imaging follow-up revealed a tumor reduction of approximately 50% as the best response. To date, the progression-free survival (PFS) has surpassed 32 months.</p><p><strong>Conclusions: </strong>To our knowledge, this is the first patient with <i>SMARCA4</i>-UT treated with this regimen. The first-line combined regimen containing immunotherapy plus antiangiogenic therapy and chemotherapy demonstrated durable treatment response in this case. This may represent a novel treatment option for this group of patients. Prospective studies will be required to validate the efficacy and safety of this therapy.</p>","PeriodicalId":17542,"journal":{"name":"Journal of thoracic disease","volume":"17 4","pages":"2730-2740"},"PeriodicalIF":2.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090140/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A prognostic nomogram based on lymph node skipping metastases in esophageal squamous cell carcinoma.","authors":"Wen-Hui Hou, Li Jie, Liao Yao, Yu-Wei Yang, He Fang, Yuan-Yuan Zhao, Xian-Yan Chen, You-Ling Gong, Xiao-Bo Du","doi":"10.21037/jtd-24-1798","DOIUrl":"10.21037/jtd-24-1798","url":null,"abstract":"<p><strong>Background: </strong>At present, the definition of lymph node skipping metastases (NSM) in esophageal squamous cell carcinoma (ESCC) is not uniform, and there were few clinical prognostic models with NSM as a factor. On the other hand, N-staging of ESCC has long been controversial. This study aimed to define NSM in ESCC and investigate its prognostic implications. Meanwhile, according to the cumulative number of cervical, thoracic and abdominal region lymph nodes, a new N-stage was defined and compared with the N-stage of American Joint Committee on Cancer/the Union for International Cancer Control (AJCC/UICC) and Japan Esophageal Society (JES).</p><p><strong>Methods: </strong>ESCC patients who underwent radical esophagectomy with lymph node metastases (LNM) between January 2012 and December 2022 at Mianyang Central Hospital and West China Hospital of Sichuan University. Patients were grouped into training and external validation cohorts. NSM was defined as any LNM outside the primary tumor region. Meanwhile, this study created a new postoperative pathology N-staging [PN(n)] based on the regional division of LNM to compare with the 8th edition of the AJCC/UICC and the 11th edition of JES N-staging.</p><p><strong>Results: </strong>There were 232 patients enrolled (training: 161; validation: 71). Cox-regression identified factors that could predict outcomes independently. Kaplan-Meier survival analysis was performed. Model performance was evaluated using the area under the receiver operating characteristic curve (AUC) and calibration plots. Independent risk factors for death included NSM [hazard ratio (HR) =1.5202], age (HR =1.036), T-stage (HR =2.874), and AJCC/UICC N stage (HR =1.9601). Prognostic models for 1-year (AUC: 0.923, 0.985), 3-year (AUC: 0.747, 0.746), and 5-year (AUC: 0.695, 0.713) survival showed high accuracy.</p><p><strong>Conclusions: </strong>NSM is associated with worse overall survival (OS) in ESCC, and the constructed prognostic model effectively predicts OS for ESCC patients.</p>","PeriodicalId":17542,"journal":{"name":"Journal of thoracic disease","volume":"17 4","pages":"1942-1957"},"PeriodicalIF":2.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prognostic indicators and nomograms for postoperative survival among younger patients with non-small cell lung cancer.","authors":"Yi Liu, Qirui Chen, Zhirong Zhang, Huandong Huo, Takuya Watanabe, Shuo Chen, Bin Hu","doi":"10.21037/jtd-2025-348","DOIUrl":"10.21037/jtd-2025-348","url":null,"abstract":"<p><strong>Background: </strong>Non-small cell lung cancer (NSCLC) diagnosed in younger patients represents a rare and distinct entity within lung cancer, yet prognostic indicators for younger patients surgically treated for NSCLC remain unclear. We aimed to analyze the long-term surgical outcomes in a large cohort and to identify predictors and to develop nomograms for effective survival prediction.</p><p><strong>Methods: </strong>The Surveillance, Epidemiology, and End Results (SEER) database [2010-2020] was queried for pathologically confirmed NSCLC cases who underwent cancer-directed surgery. We selected a cutoff age of 49 years or younger to define the younger cohort. The Kaplan-Meier method was used for survival analysis. Cox proportional hazards regression models were used to determine prognostic parameters associated with survival. Nomogram performance was assessed via receiver operating characteristic (ROC) curves and calibration curves in both the training and validation cohort.</p><p><strong>Results: </strong>Among the 2,584 younger patients surgically treated for NSCLC meeting the inclusion criteria, the 5-year overall survival (OS) and lung cancer-specific survival (LCSS) rates were 84.3% and 87.0%, respectively. Multivariate analysis identified age, gender, histology, T stage, tumor, node, metastasis (TNM) stage, and postoperative therapy as independent prognosticators. Nomograms exhibited robust predictive performance. The ROC areas for 5-year OS were 0.816 for the training cohort and 0.811 for the validation cohort, while for the 5-year LCSS, the areas were 0.845 and 0.848, respectively. Additionally, the calibration curves demonstrated a high degree of concordance between the actual and predicted values.</p><p><strong>Conclusions: </strong>We identified the independent survival factors among younger patients treated surgically for NSCLC and established nomograms for the prediction of the long-term survival, offering valuable insights into clinical decision-making for post-surgical treatment.</p>","PeriodicalId":17542,"journal":{"name":"Journal of thoracic disease","volume":"17 4","pages":"2365-2376"},"PeriodicalIF":2.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090160/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prognostic role of subsolid ground-glass opacity, pure ground-glass opacity, and solid nodules of the lung: a retrospective observational study.","authors":"Lorenzo Federico Zini Radaelli, Elisabetta Fabbri, Matteo Costantini, Michele Gaudio, Alessandra Dubini, Emanuela Giampalma, Franco Stella, Beatrice Aramini","doi":"10.21037/jtd-24-1825","DOIUrl":"10.21037/jtd-24-1825","url":null,"abstract":"<p><strong>Background: </strong>Lung nodules can be classified as solid nodules and ground-glass opacity nodules (GGO-GGN). A GGO nodule is a radiological finding characterized by a faded opacity that may hide a preinvasive or invasive adenocarcinoma. GGOs can be divided into two categories: pure GGO (pGGN) and mixed/subsolid GGO (mGGN). The transformation of GGO into solid nodules is a strong indicator of malignancy. Current guidelines suggest a 5-year chest computed tomography (CT) follow-up (FU) for both pure and subsolid GGOs. This study aimed to analyze the prognosis of patients undergoing major lung resection at our center in relation to the radiological characteristics of the resected nodule to assess how much the nodule density in GGO may affect the prognosis.</p><p><strong>Methods: </strong>This retrospective observational study analyzed 133 patients underwent lobectomy at our center between 2010 and 2020. The nodule density was assessed by CT images, classifying into three groups according to the consolidation tumor ratio (CTR): group 1: pure GGO (pGGN; CTR <0.5, n=30); group 2: subsolid nodule (mGGN; 0.5≤ CTR <1, n=37), group 3: solid nodule (CTR =1, n=66). Overall survival (OS) was calculated from the date of surgery until death or last FU. The OS was estimated through Kaplan-Meier curves, the log-rank test was used for univariate analysis, and Cox regression was used for multivariate analysis. Values with P<0.05 were considered statistically significant.</p><p><strong>Results: </strong>Of 133 patients, the OS, 5 years after surgery and related to the nodule density, has been classified into three groups as: group 1 contained 30 patients with pure GGO nodules, with a 5-year survival rate of 96% [95% confidence interval (CI): 73-99%]; group 2 contained 37 patients with subsolid GGOs, with a 5-year survival rate of 76% (95% CI: 56-88%); group 3 contained 66 patients with solid nodules, with a 5-year survival rate of 78% (95% CI: 62-88%) with median survival time was 95 months. Multivariate analysis with age and FU lasting for over 6 months in the Cox model confirmed that density was a risk factor, with hazard ratio (HR) =8.37 (95% CI: 1.03-68.12) for group 2 <i>vs.</i> group 1 and HR =8.66 (95% CI: 1.06-70.90) for group 3 <i>vs.</i> group 1. A FU exceeding 6 months after diagnosis was not a significant risk factor (P=0.57), whereas age was a significant risk factor (HR =1.07, 95% CI: 1.001-1.13).</p><p><strong>Conclusions: </strong>For pure GGO long-term FU is justified, whereas surgery should be considered as the first option for subsolid nodules. This retrospective study provides a foundation for further research to better define the most appropriate approach to subsolid nodules.</p>","PeriodicalId":17542,"journal":{"name":"Journal of thoracic disease","volume":"17 4","pages":"2239-2247"},"PeriodicalIF":2.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell analysis and machine learning-based integration develop an immune-responsive signature of antigen-presenting cancer-associated fibroblasts in lung adenocarcinoma.","authors":"Weijiao Xu, Haitang Yang, Feng Yao","doi":"10.21037/jtd-2024-2015","DOIUrl":"10.21037/jtd-2024-2015","url":null,"abstract":"<p><strong>Background: </strong>Cancer-associated fibroblasts (CAFs) are pivotal regulators of the tumor immune microenvironment, shaping immune responses and influencing therapeutic outcomes. While previous studies have predominantly focused on CAF subpopulations that impair responses to immune checkpoint inhibitors (ICIs), CAF subsets associated with favorable ICIs responses in lung adenocarcinoma (LUAD) remain underexplored. In this study, we integrated bulk RNA and single-cell RNA sequencing data from LUAD samples to identify CAF subpopulations relevant to ICIs efficacy.</p><p><strong>Methods: </strong>Using a machine learning-driven approach, we developed a robust immune response signature based on this antigen-presenting CAFs (apCAFs) subset to predict ICIs responses.</p><p><strong>Results: </strong>We uncovered a novel subset of apCAFs exhibiting macrophage-like features, characterized by the expression of major histocompatibility complex (MHC) class II, CD74, and costimulatory molecules (CD80, CD86, CD83, and CD40). This subset, distinct from classic apCAFs described in other cancer types, is strongly associated with favorable ICIs responses across multiple datasets. Notably, these macrophage-like apCAFs are present in LUAD samples prior to treatment, although their abundance varies among individuals. Patients classified as high-risk using signature calculated by a machine learning-driven approach exhibited lower overall survival rates and diminished immune cell infiltration following ICIs therapy.</p><p><strong>Conclusions: </strong>Collectively, our findings establish a critical link between macrophage-like apCAFs and ICIs efficacy, offering a clinically applicable signature for patient stratification and guiding therapeutic strategies targeting the tumor microenvironment.</p>","PeriodicalId":17542,"journal":{"name":"Journal of thoracic disease","volume":"17 4","pages":"2321-2338"},"PeriodicalIF":2.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The management of type 2 inflammatory respiratory diseases: a Chinese expert consensus [2024].","authors":"Nan Jia, Meiling Jin, Yun Liu, Nan Su, Ying Sun, Wei Tang, Gang Wang, Hua Xie, Jiaxing Xie, Min Xie, Xin Yao, Huanping Zhang, Ruchong Chen, Chuntao Liu, Jing Li","doi":"10.21037/jtd-2024-2092","DOIUrl":"10.21037/jtd-2024-2092","url":null,"abstract":"<p><strong>Background: </strong>Type 2 (T2) inflammatory respiratory diseases encompass a range of conditions characterized by inflammation affecting the airways and lung parenchyma, with their pathogenesis rooted in T2 inflammation. Biological treatments that mitigate T2 inflammation revolutionize the therapeutic landscape for these respiratory diseases. However, there are decision-making difficulties in terms of the target population, timing of initiation, and type selection for biological targeted therapy.</p><p><strong>Methods: </strong>Search strategies were focused on relevant issues related to T2 inflammatory respiratory diseases from PubMed with search date from 2014 to 2024. The quality of evidence and grading recommendations were assessed with the Grading of Recommendations Assessment, Development and Evaluation (GRADE) system. Consensus was achieved through two rounds of anonymous voting with a strong recommendation demanding at least 70% approval from the participants.</p><p><strong>Results: </strong>A total of 370 basic research results and clinical evidence-based medical data were collected and reviewed. The latest research advances, clinical evidence, and expert insights relating to the use of biological treatments aiming at T2 inflammation in respiratory diseases and their co-morbidities were discussed rigorously and iteratively by an expert panel, and a consensus report with recommendations is presented.</p><p><strong>Conclusions: </strong>This consensus outlines the pathogenesis, assessment of T2 inflammation, biological therapies targeted at T2 inflammation, and management strategies for T2 inflammatory respiratory diseases and their comorbidities. It will serve as a valuable guide for clinicians in China, empowering them to diagnose and manage these conditions more effectively.</p>","PeriodicalId":17542,"journal":{"name":"Journal of thoracic disease","volume":"17 4","pages":"1807-1831"},"PeriodicalIF":2.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144119446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine learning algorithms for predicting malignancy grades of lung adenocarcinoma and guiding treatments: CT radiomics-based comparisons.","authors":"Jun Zhu, Jiayu Tao, Fengfeng Zhang, Jie Yao, Ke Chen, Yuxuan Wang, Xiaochen Lu, Bin Ni, Maoshan Zhu","doi":"10.21037/jtd-2025-310","DOIUrl":"10.21037/jtd-2025-310","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Lung adenocarcinoma (LUAD) is the most frequently diagnosed subtype of non-small cell lung cancer (NSCLC). Notably, prognosis can vary significantly among LUAD patients with different tumor subtypes. The advent of radiomics and machine learning (ML) technologies enables the development of non-invasive pathology predictive models. We attempted to develop computed tomography (CT) radiomics-based diagnostic models, enhanced by ML, to predict LUAD malignancy grade and guide surgical strategies.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;In this retrospective analysis, a total of 168 surgical patients with histology-confirmed LUAD were divided into low-risk group (n=93) and intermediate-to-high-risk group (n=75) based on postoperative pathology. The region of interest (ROI) was delineated on the preoperative CT images for all patients, followed by the extraction of radiomic features. Patients were randomly allocated to a training set (n=117) and a testing set (n=51) in a 7:3 ratio. Within the training set, clinical-radiological model (CM) and radiomics model (RM) were developed utilizing patients' clinical characteristics, radiological semantic features, and radiomic features, along with the calculation of Rad scores. After the Rad scores were combined with independent risk factors among clinical-radiological features, logistic regression (LR), decision tree (DT), random forest (RF), extreme gradient boosting (XGBoost), support vector machine (SVM), K-nearest neighbors (KNN), and naïve Bayes model (NBM) were employed to create different comprehensive models (COMs). The optimal model was identified based on the receiver operating characteristic (ROC) curves and the DeLong test. Finally, Shapley additive explanations (SHAP) were utilized to visualize the predictive processes of the models.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Among the 168 patients enrolled, there were 50 males (29.76%) aged 56 (49.25, 67.00) years and 118 females (70.24%) aged 56.5 (42.00, 64.00) years; Diameter (P&lt;0.001), and consolidation-to-tumor ratio (CTR) ≥0.5 (P=0.002) were identified as independent risk factors for the malignancy degree of LUAD during CM creation. The CM had an area under the ROC curve (AUC) of 0.909 [95% confidence interval (CI): 0.856-0.962] in the training set and 0.920 (95% CI: 0.846-0.994) in the testing set. The RM, comprising seven radiomic features, achieved an AUC of 0.961 (95% CI: 0.926-0.996) in the training set and 0.957 (95% CI: 0.905-1.000) in the testing set. Among models created using various ML algorithms, the XGBoost model was identified as the optimal model. SHAP visualization revealed the model prediction processes and the values of different features.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;We constructed and validated a robust, integrative model leveraging ML and CT radiomics, which amalgamates radiomics, clinical, and radiological attributes to precisely identify LUADs with elevated postoperative pathological grades. This enab","PeriodicalId":17542,"journal":{"name":"Journal of thoracic disease","volume":"17 4","pages":"2423-2440"},"PeriodicalIF":2.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144119917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of novel dark-quencher labeled probes in multiplex qRT-PCR assays for rapid detection of SARS-CoV-2 variants.","authors":"Zhiqi Zeng, Jie Yang, Jun Dai, Lirong Zou, Zhengshi Lin, Yong Liu, Wenda Guan, Feng Li, Kui Zheng, Shuai Yuan, Fangfang Sun, Fengxia He, Ye Hong, Hui Li, Wei Liu, Guangqi Men, Xinyue Zhang, Yun Lan, Xizi Deng, Liya Li, Yaqing Lin, Honghao Lai, Peng Qian, Qinghong Fan, Mengling Jiang, Jiaojiao Li, Guofang Tang, Qiaohui Mo, Xiaoyan Deng, Jicheng Huang, Xiaoling Deng, Zifeng Yang","doi":"10.21037/jtd-24-853","DOIUrl":"10.21037/jtd-24-853","url":null,"abstract":"<p><strong>Background: </strong>Coronavirus disease 2019 (COVID-19) is an acute infectious disease caused by the new coronavirus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Because SARS-CoV-2 frequently mutates, it creates a number of variants that must be distinguished and tracked using a rapid detection technique. At present, the identification of virus variants often requires sequencing of the viral genome with sophisticated techniques which are costly and time-consuming. On the other hand, the quantitative reverse transcription-polymerase chain reaction (qRT-PCR) method used to diagnose SARS-CoV-2 infection has been widely applied worldwide amid COVID-19 pandemic. Due to the lower specificity and sensitivity in detecting different strains using multiple qRT-PCR, we aimed to develop novel dark quencher (DQ) labeled probes to improve the performance of multiple qRT-PCR. DQ probes are dihydropyrroloindole carboxylate (DPI3)-analogue.</p><p><strong>Methods: </strong>We first tested their amplification efficiency and specificity, on detecting single nucleotide polymorphism through qRT-PCR, and the simultaneous detection efficiency of multiple SARS-CoV-2 mutation sites. The DQ labeled probes were further applied in multiplex qRT-PCR assays, and the method was validated on SARS-CoV-2 positive clinical samples for its sensitivity and specificity.</p><p><strong>Results: </strong>DQ probes exhibited better specificity and sensitivity than the TaqMan^® Minor Groove Binder (MGB) and TaqMan probes. Great analytical sensitivity (limit of detection of 250 copies/mL), good specificity (no cross-reaction with other pathogens), and great clinical performance (99.4-100% consistency with next-generation sequencing) were demonstrated by the designed multiplex qRT-PCR tests.</p><p><strong>Conclusions: </strong>Our novel DQ-probe/multiplex qRT-PCR assay provides a rapid and simple method to quickly distinguish SARS-CoV-2 variants, we were able to quickly identify SARS-CoV-2 variants (Delta and Omicron BA.1, BA.1.1, BA.2, BA.2.12.1, BA.3, BA.4, and BA.5) that target nine specific mutation sites in the <i>ORF</i>, <i>N</i>, <i>NSP1</i>, <i>NSP3</i>, and <i>S</i> genes.</p>","PeriodicalId":17542,"journal":{"name":"Journal of thoracic disease","volume":"17 4","pages":"2159-2173"},"PeriodicalIF":2.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144119948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}